| Entry | Gene Names | Organism | Function [CC] | Protein names | Gene Ontology (molecular function) | Subcellular location [CC] | Reviewed | Entry Name | Cofactor | Catalytic activity | pH dependence | Pathway | EC number | Temperature dependence | Transmembrane | Intramembrane | Protein families |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| P40227 | CCT6A CCT6 CCTZ | Homo sapiens (Human) | FUNCTION: Component of the chaperonin-containing T-complex (TRiC), a molecular chaperone complex that assists the folding of proteins upon ATP hydrolysis (PubMed:25467444). The TRiC complex mediates the folding of WRAP53/TCAB1, thereby regulating telomere maintenance (PubMed:25467444). The TRiC complex plays a role in the folding of actin and tubulin (Probable). {ECO:0000269|PubMed:25467444, ECO:0000305}. | T-complex protein 1 subunit zeta (TCP-1-zeta) (Acute morphine dependence-related protein 2) (CCT-zeta-1) (HTR3) (Tcp20) | ATP binding [GO:0005524]; ATP hydrolysis activity [GO:0016887]; ATP-dependent protein folding chaperone [GO:0140662]; protein folding chaperone [GO:0044183]; RNA binding [GO:0003723]; unfolded protein binding [GO:0051082]; WD40-repeat domain binding [GO:0071987] | SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:8034610}. | reviewed | TCPZ_HUMAN | NA | NA | NA | NA | NA | NA | NA | NA | TCP-1 chaperonin family |
| Q9NP81 | SARS2 SARSM | Homo sapiens (Human) | FUNCTION: Catalyzes the attachment of serine to tRNA(Ser). Is also probably able to aminoacylate tRNA(Sec) with serine, to form the misacylated tRNA L-seryl-tRNA(Sec), which will be further converted into selenocysteinyl-tRNA(Sec). {ECO:0000250|UniProtKB:Q9N0F3}. | Serine–tRNA ligase, mitochondrial (EC 6.1.1.11) (SerRSmt) (Seryl-tRNA synthetase) (SerRS) (Seryl-tRNA(Ser/Sec) synthetase) | ATP binding [GO:0005524]; RNA binding [GO:0003723]; serine-tRNA ligase activity [GO:0004828]; tRNA binding [GO:0000049] | SUBCELLULAR LOCATION: Mitochondrion matrix {ECO:0000250|UniProtKB:Q9N0F3}. | reviewed | SYSM_HUMAN | NA | CATALYTIC ACTIVITY: Reaction=ATP + L-serine + tRNA(Ser) = AMP + diphosphate + H(+) + L-seryl-tRNA(Ser); Xref=Rhea:RHEA:12292, Rhea:RHEA-COMP:9669, Rhea:RHEA-COMP:9703, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616, ChEBI:CHEBI:33019, ChEBI:CHEBI:33384, ChEBI:CHEBI:78442, ChEBI:CHEBI:78533, ChEBI:CHEBI:456215; EC=6.1.1.11; Evidence={ECO:0000250|UniProtKB:Q9N0F3}; CATALYTIC ACTIVITY: Reaction=ATP + L-serine + tRNA(Sec) = AMP + diphosphate + H(+) + L-seryl-tRNA(Sec); Xref=Rhea:RHEA:42580, Rhea:RHEA-COMP:9742, Rhea:RHEA-COMP:10128, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616, ChEBI:CHEBI:33019, ChEBI:CHEBI:33384, ChEBI:CHEBI:78442, ChEBI:CHEBI:78533, ChEBI:CHEBI:456215; EC=6.1.1.11; Evidence={ECO:0000250|UniProtKB:Q9N0F3}; | NA | PATHWAY: Aminoacyl-tRNA biosynthesis; selenocysteinyl-tRNA(Sec) biosynthesis; L-seryl-tRNA(Sec) from L-serine and tRNA(Sec): step 1/1. | 6.1.1.11 | NA | NA | NA | Class-II aminoacyl-tRNA synthetase family, Type-1 seryl-tRNA synthetase subfamily |
| Q99KN1 | Arrdc1 | Mus musculus (Mouse) | FUNCTION: Functions as an adapter recruiting ubiquitin-protein ligases to their specific substrates (PubMed:23886940, PubMed:27462458). Through an ubiquitination-dependent mechanism plays for instance a role in the incorporation of SLC11A2 into extracellular vesicles (PubMed:27462458). More generally, plays a role in the extracellular transport of proteins between cells through the release in the extracellular space of microvesicles (By similarity). By participating to the ITCH-mediated ubiquitination and subsequent degradation of NOTCH1, negatively regulates the NOTCH signaling pathway (PubMed:23886940). {ECO:0000250|UniProtKB:Q8N5I2, ECO:0000269|PubMed:23886940, ECO:0000269|PubMed:27462458}. | Arrestin domain-containing protein 1 (Alpha-arrestin 1) | arrestin family protein binding [GO:1990763]; identical protein binding [GO:0042802]; ubiquitin ligase-substrate adaptor activity [GO:1990756]; ubiquitin protein ligase binding [GO:0031625] | SUBCELLULAR LOCATION: Cell membrane {ECO:0000250|UniProtKB:Q8N5I2}. Note=Also found in extracellular vesicles different from exosomes. {ECO:0000250|UniProtKB:Q8N5I2}. | reviewed | ARRD1_MOUSE | NA | NA | NA | NA | NA | NA | NA | NA | Arrestin family |
| Q8WZB0 | ERCC6L2-AS1 C9orf130 LINC00476 NAG12 | Homo sapiens (Human) | NA | Putative uncharacterized protein ERCC6L2-AS1 (ERCC6L2 antisense RNA 1) (Nasopharyngeal carcinoma-associated gene 12 protein) | NA | NA | reviewed | CI130_HUMAN | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| Q5EE38 | Acd | Mus musculus (Mouse) | FUNCTION: Component of the shelterin complex (telosome) that is involved in the regulation of telomere length and protection. Shelterin associates with arrays of double-stranded TTAGGG repeats added by telomerase and protects chromosome ends. Without its protective activity, telomeres are no longer hidden from the DNA damage surveillance and chromosome ends are inappropriately processed by DNA repair pathways. Promotes binding of POT1 to single-stranded telomeric DNA. Modulates the inhibitory effects of POT1 on telomere elongation. The ACD-POT1 heterodimer enhances telomere elongation by recruiting telomerase to telomeres and increasing its processivity (By similarity). May play a role in organogenesis (PubMed:15537664). {ECO:0000250|UniProtKB:Q96AP0, ECO:0000269|PubMed:15537664}. | Adrenocortical dysplasia protein | DNA polymerase binding [GO:0070182]; protein-containing complex binding [GO:0044877]; telomeric DNA binding [GO:0042162] | SUBCELLULAR LOCATION: Nucleus {ECO:0000250|UniProtKB:Q96AP0}. Chromosome, telomere {ECO:0000250|UniProtKB:Q96AP0}. | reviewed | ACD_MOUSE | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| Q8N3U4 | STAG2 SA2 | Homo sapiens (Human) | FUNCTION: Component of cohesin complex, a complex required for the cohesion of sister chromatids after DNA replication. The cohesin complex apparently forms a large proteinaceous ring within which sister chromatids can be trapped. At anaphase, the complex is cleaved and dissociates from chromatin, allowing sister chromatids to segregate. The cohesin complex may also play a role in spindle pole assembly during mitosis. {ECO:0000269|PubMed:12034751}. | Cohesin subunit SA-2 (SCC3 homolog 2) (Stromal antigen 2) | chromatin binding [GO:0003682] | SUBCELLULAR LOCATION: Nucleus. Chromosome. Chromosome, centromere. Note=Associates with chromatin. Before prophase it is scattered along chromosome arms. During prophase, most of cohesin complexes dissociate from chromatin probably because of phosphorylation by PLK1, except at centromeres, where cohesin complexes remain. At anaphase, the RAD21 subunit of cohesin is cleaved, leading to the dissociation of the complex from chromosomes, allowing chromosome separation. In germ cells, cohesin complex dissociates from chromatin at prophase I, and may be replaced by a meiosis-specific cohesin complex. | reviewed | STAG2_HUMAN | NA | NA | NA | NA | NA | NA | NA | NA | SCC3 family |
| Q9D8B4 | Ndufa11 | Mus musculus (Mouse) | FUNCTION: Accessory subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I), that is believed not to be involved in catalysis. Complex I functions in the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone. {ECO:0000250|UniProtKB:Q86Y39}. | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 (Complex I-B14.7) (CI-B14.7) (NADH-ubiquinone oxidoreductase subunit B14.7) | NA | SUBCELLULAR LOCATION: Mitochondrion inner membrane {ECO:0000250|UniProtKB:Q86Y39}; Multi-pass membrane protein {ECO:0000255}; Matrix side {ECO:0000250|UniProtKB:Q86Y39}. | reviewed | NDUAB_MOUSE | NA | NA | NA | NA | NA | NA | TRANSMEM 21..43; /note=“Helical”; /evidence=“ECO:0000255”; TRANSMEM 58..80; /note=“Helical”; /evidence=“ECO:0000255” | NA | Complex I NDUFA11 subunit family |
| A2A6Q5 | Cdc27 | Mus musculus (Mouse) | FUNCTION: Component of the anaphase promoting complex/cyclosome (APC/C), a cell cycle-regulated E3 ubiquitin ligase that controls progression through mitosis and the G1 phase of the cell cycle. The APC/C complex acts by mediating ubiquitination and subsequent degradation of target proteins: it mainly mediates the formation of ‘Lys-11’-linked polyubiquitin chains and, to a lower extent, the formation of ‘Lys-48’- and ‘Lys-63’-linked polyubiquitin chains (By similarity). {ECO:0000250}. | Cell division cycle protein 27 homolog | protein phosphatase binding [GO:0019903] | SUBCELLULAR LOCATION: Nucleus {ECO:0000250|UniProtKB:P30260}. Cytoplasm, cytoskeleton, spindle {ECO:0000250|UniProtKB:P30260}. | reviewed | CDC27_MOUSE | NA | NA | NA | PATHWAY: Protein modification; protein ubiquitination. | NA | NA | NA | NA | APC3/CDC27 family |
| P31254 | Uba1y Sby Ube1ay Ube1y Ube1y1 | Mus musculus (Mouse) | FUNCTION: Activates ubiquitin by first adenylating its C-terminal glycine residue with ATP, and thereafter linking this residue to the side chain of a cysteine residue in E1, yielding a ubiquitin-E1 thioester and free AMP (By similarity). The Y chromosome form could be involved in the survival and proliferation of differentiating spermatogonia. {ECO:0000250|UniProtKB:P22314, ECO:0000305}. | Ubiquitin-like modifier-activating enzyme 1 Y (EC 6.2.1.45) (Ubiquitin-activating enzyme E1) (Ubiquitin-activating enzyme E1 Y) | ATP binding [GO:0005524]; ubiquitin activating enzyme activity [GO:0004839] | NA | reviewed | UBA1Y_MOUSE | NA | CATALYTIC ACTIVITY: Reaction=ATP + ubiquitin + [E1 ubiquitin-activating enzyme]-L-cysteine = AMP + diphosphate + S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine.; EC=6.2.1.45; Evidence={ECO:0000250|UniProtKB:P22314}; | NA | PATHWAY: Protein modification; protein ubiquitination. {ECO:0000250|UniProtKB:P22314}. | 6.2.1.45 | NA | NA | NA | Ubiquitin-activating E1 family |
| Q8NBR0 | TP53I13 DSCP1 | Homo sapiens (Human) | FUNCTION: May act as a tumor suppressor. Inhibits tumor cell growth, when overexpressed. {ECO:0000269|PubMed:14767535}. | Tumor protein p53-inducible protein 13 (Damage-stimulated cytoplasmic protein 1) | NA | SUBCELLULAR LOCATION: Cell membrane {ECO:0000305}; Single-pass type I membrane protein {ECO:0000305}; Extracellular side {ECO:0000305}. Cytoplasm {ECO:0000269|PubMed:14767535}. Note=Associates with unknown subcellular structures in the cytoplasm. | reviewed | P5I13_HUMAN | NA | NA | NA | NA | NA | NA | TRANSMEM 310..330; /note=“Helical”; /evidence=“ECO:0000255” | NA | NA |
Comparison of proteins in humans and mice
Anton Wang (s183220), Line (s184242), Jeppe (s213426), Oscar (s193775) and Johan (s225001)
Introduction
The mouse as a model organism
Differences/similarities in protein location, role and more between mice and humans.
Summary statistics on clean data and more elaborate analysis on augmented data
Materials
- Gene ontology and amino acid seq data from swiss-prot reviewed uniprot data
- The entries was very untidy and had to be wrangled a lot
- An example of one of the raw data files:
Materials
Variables to describe proteins in humans and mice
[1] "Entry" "Reviewed"
[3] "Entry Name" "Gene Names"
[5] "Organism" "Protein names"
[7] "Cofactor" "Catalytic activity"
[9] "pH dependence" "Pathway"
[11] "Function [CC]" "EC number"
[13] "Temperature dependence" "Gene Ontology (molecular function)"
[15] "Subcellular location [CC]" "Transmembrane"
[17] "Intramembrane" "Protein families" and Methods
Overview of workflow
Results - Length and Mass
- Preliminary summary statistics of protein length and mass distributions in mice and humans clearly show their similarity as organisms.
Results - Length, Cofactors and Enzyme Classes
Enzyme classes in subcellular locations
Almost identical logo plots for mouse and human enzymes
| entry | organism | enzyme_class | logo_seq |
|---|---|---|---|
| O95278 | human | transferase | QGDSGGP |
| … | … | … | … |
| P27708 | human | hydrolase | STYEKHL |
| Q2L4Q9 | human | lyase | AIVDKRV |
Table: Organism == human & enzyme_class != NA
| entry | organism | enzymeclass | logo_seq |
|---|---|---|---|
| Q8K0D2 | mouse | isomerase | QGDSGGP |
| … | … | … | … |
| Q91ZA3 | mouse | hydrolase | STYEKHL |
| Q9EQW8 | mouse | transferase | AIVDKRV |
Table: Organism == mouse & enzyme_class != NA
Discussion
The process
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Human and mice enzymes are very similar
Data from UniProt
Could also “zoom in” and examine more specific proteins/enzymes
UniProt contain data for many other organisms